No abstract

Haplotype analysis is important for mapping traits. Recently, methods for estimating haplotype frequencies from genotypes of unrelated individuals based on the expectation-maximization (EM) algorithm have been developed. Our program estimates haplotype frequencies in the population and determines the posterior probability distribution of diplotype configuration (diplotype distribution) for each subject based on the estimated haplotype frequencies. Samples from three ethnic groups for the smoothelin gene (SMTN ) and those from three Japanese groups for serum amyloid A genes (SAA!) were analyzed. The estimated diplotype distribution for each individual was concentrated, in most cases, in a single diplotype configuration. The diplotype configuration thus determined was the same as that determined in in vitro experiments, with one exception. Thus, the diplotype configurations determined using the estimated haplotype frequencies from unrelated individuals are reliable. Using this method, the risk of a subject developing a phenotype may be estimated from the diplotype distribution when the phenotype is associated with diplotype configurations. Haplotype information is expected to be important for mapping disease-associated genes and for selecting markers to estimate efficiently the relative risks of individuals to show specific phenotypes such as diseases. The complete information can be obtained from the diplotype configuration (combination of two haplotypes ; designated genotype in Excoffier & Slatkin, 1995) for each individual. Usually, however, the phase data are not available and partial information can be obtained from the genotypes at related

Janus kinases (Jaks) are a small family of cytoplasmic tyrosine kinases, critical for signaling by Type I and II cytokine receptors. The importance of Jaks in signaling by these receptors has been firmly established by analysis of mutant cell lines, the generation of Jak knock-out mice, and the identification of patients with Jak3 mutations. While a number of other ligands that do not bind Type I and II cytokine receptors have also been reported to activate Jaks, the requirement for Jaks in signaling by these receptors is less clear. Chemokines for example, which bind seven transmembrane receptors, have been reported to activate Jaks, and principally through the use of pharmacological inhibitors, it has been argued that Jaks are essential for chemokine signaling. In the present study, we focused on CXCR4, which binds the chemokine CXCL12 or stromal cell-derived factor-1, a chemokine that has been reported to activate Jak2 and Jak3. We found that the lack of Jak3 had no effect on CXCL12 signaling or chemotaxis nor did overexpression of wild-type versions of the kinase. Similarly, overexpression of wild-type or catalytically inactive Jak2 or "knocking-down" Jak2 expression using siRNA also had no effect. We also found that in primary lymphocytes, CXCL12 did not induce appreciable phosphorylation of any of the Jaks compared with cytokines for which these kinases are required. Additionally, little or no Stat (signal transducer and activator of transcription) phosphorylation was detected. Thus, we conclude that in contrast to previous reports, Jaks, especially Jak3, are unlikely to play an essential role in chemokine signaling.

To examine whether polymorphism at the SAA loci is associated with the development of amyloid protein A (AA)-amyloidosis, we determined the genotypes at the SAA1 and SAA2 loci in 43 AA-amyloidosis patients (amyloidosis population) and 77 patients with rheumatoid arthritis (RA) who had been ill for less than 5 years (early RA population). We also compared the frequencies of the genotypes at the SAA1 locus among 90 Korean, 95 Taiwanese, and 103 Japanese healthy subjects. The frequencies of the gamma/gamma genotype and gamma alleles at the SAA1 locus were significantly higher in the amyloidosis population than in the early RA population (34.9% versus 7.8%, and 58.1% versus 33.8%, chi2 test P=0.0001). The frequencies of the gamma allele at the SAA1 locus in Koreans, Taiwanese, and Japanese were 41.6%, 35.6%, and 37.4%, respectively. The length of the latent period of AA-amyloidosis was significantly longer in the patients with smaller numbers of the gamma allele at the SAA1 locus (Spearman's correlation coefficient: -0.42, P<0.05). On the other hand, the mean C-reactive protein (CRP) level during 2 years prior to the diagnosis of AA-amyloidosis was significantly higher in the patients with larger numbers of the gamma allele at the SAA1 locus (Spearman's correlation coefficient: 0.34, P<0.05). No significant association was found between amyloidosis and polymorphism at the SAA2 locus. We postulate that the allele SAA1gamma renders an RA patient susceptible to amyloidosis, possibly by affecting the severity of inflammation in RA.